Implications of Matter
by Morvram
Summary: This is a retelling of the events following the end of Mass Effect 1. Instead of Shepard dying and immediately being resurrected during the opening scenes by a terrorist group which he promptly starts working for, Shepard and crew have spent the past five years searching for further information about the Reapers, before being summoned to a new mission by the Council.


_Implications of Matter: Chapter 1_

 _The Spectre_

The night after the summons, I dream of Ilos.

My crew and I had tracked down the Conduit, knowing that Saren might be there before we arrived. Saren - once a Spectre, now a slave to the machines that sought the destruction of all advanced civilizations in the galaxy, for reasons unknown to us and - if Sovereign's taunts were to be believed - unknowable. Incomprehensible to the organic mind.

Urdnot Wrex and Lieutenant Kaidan Alenko led the charge through swarms of Geth, which Saren had brought to Ilos to guard the underground archives and the Conduit. Dr. Liara T'Soni, Tali'Zorah nar Rayya, and I followed them into the depths below Ilos's surface, where we found...

Vigil. An ancient Prothean VI. It told us the truth about Ilos, the Conduit, and the Reapers - it revealed to us the origins of the Mass Relays and the Citadel itself, built by the Reapers to ensure that all sufficiently advanced galactic civilizations would gather together in one place.

We emerged from that chamber, filled with the defunct life-support pods of thousands upon thousands of long-gone Protheans, boarded the Mako, and drove straight down the hill that led from the exit of the archive to the Conduit, a mass relay built right into the planet's surface, pointed straight into the sky. And, driving directly into the Mass Relay, we emerged into the Presidium on the Citadel, near the Council Chambers.

There are further flashes of that day's events: the fight through the Presidium to reach the audience chamber where the Council met, where I had been made a Spectre not long before. Saren's moment of realization, the terror in his eyes as his mind fully reasserted itself over the programming put in place by long exposure to Sovereign. The moment when he made his final decision, knowing he had only seconds before Sovereign regained control.

A single roaring gunshot, and then the crash of Saren's body falling through the pane of glass beneath the Citadel Council's podiums.

I awaken in my captain's chambers with sweat running down my face.

The only sound around me is the ambient humming of the dim lights in my room - not so bright that it would prevent me from sleeping, but just bright enough that I would be able to clearly see anybody entering the room uninvited. Not that they would be able to do so without great difficulty, but the little bit of light helps me to feel more secure in my bedroom aboard the Normandy.

With a sigh, I glance over at the clock. It's five in the morning according to the twenty-five-hour galactic standard clock. Early. Even earlier than I've gotten used to getting up on the search for any useful information about the Reapers that I have been conducting for the past five years.

It's been a fruitless search, and that is why the Council has decided it's time to give me another mission. That must be the purpose of the summons to the Citadel, for which we are currently hurtling at faster-than-light speeds toward the nearest Mass Relay, which will take us straight to the Citadel. I am a Spectre, after all. A member of the Council's Office of Special Tactics and Reconnaissance, I am able to operate outside the procedures which govern most police forces and militaries in Council Space. But those rights come with additional responsibilities - namely, the Council is free to send me on whatever missions they believe require the… shall we say, _subtle_ touch of a Council Spectre.

Whatever the mission they are going to send me on, I simply hope that I will still be able to pursue my investigation into the Reapers. Sovereign may have been destroyed during its ill-fated attack on the Citadel, the Geth armies it managed to control routed and retreated back behind the Perseus Veil, but if it was telling the truth, if Vigil was telling the truth, and if my visions are anything to go by, then there are thousands more of them out there. All the Council's fleets combined were hardly able to take down one. If the Reapers ever emerge in full force, galactic civilization won't stand a chance.

After showering and dressing myself in a standard black uniform with white trim joining the garment along a curved line running up the center of my chest and toward my left shoulder, I emerge from the captain's quarters and head toward the elevator leading from crew quarters to the mess hall beneath the Normandy's bridge. I pass Kaidan and Doctor Chakwas standing out in the hallway, speaking quietly to one another, and nod a greeting in their direction. Chakwas looks up with an expression of concern on her face and Kaidan stops mid-sentence, turning toward me. "Captain." He pops off a quick salute. "You look exhausted. The night crew is down on the Bridge if that's where you are headed."

"I didn't sleep well at all," I admit. "But I'm not going to the bridge. I'm going to get breakfast. If I can't rest properly before meeting with the Council, I might as well not go before them with my stomach rumbling. Want to join me?"

"Of course, Captain," Kaidan replies, and falls in step beside me.

"Captain Shepard," Doctor Chakwas calls as we move away from her. "I can issue you some medication to help you sleep this morning, if you'd like. We won't be at the Citadel until mid-afternoon."

I take a moment to consider the offer, then shrug. "I'll take you up on that in an hour or two, I suppose. As long as it won't leave me groggy when we do get there."

On the elevator, Kaidan stands loosely, arms resting with hands on his thighs and his whole body leaning slightly toward the wall to his right. Almost as soon as the door closes, he turns to me. "Odd that the Council is calling you to the Citadel in person for this meeting, isn't it?" he comments. "I mean, they haven't asked to meet with you in person in five years. Status reports via the extranet have been enough."

This occurred to me yesterday, but I didn't say anything out loud about it. Now, there's no reason not to say something. "I believe they have a new mission for me. Something secret, that they don't want intercepted. Asking for updates on our search for information about the Reapers isn't as sensitive as some of the other missions they might put us to."

"I suppose," Kaidan said. "As long as the Reapers aren't listening in on your chats with the Council." He chuckles nervously, then shakes his head with a sigh. "No. They're all stuck out in dark space, or we wouldn't be here having this conversation."

The elevator door opens and I step out into the room, followed by Kaidan. One floor beneath the bridge of the Normandy is a wide-open space with a table in the center, and a small kitchen off to the side of that. Further from the dining area and kitchen are the ship's armory, med bay, and a few private offices like the one where Liara T'Soni works. Probably writing yet another defense of her treatise about the fall of the Prothean civilization.

I pull out a chair and sit at the table dominating this space, then lean back and put my feet up on the surface, waving my hand vaguely in Kaidan's direction. I can feel an involuntary, lopsided grin touch my lips as Lieutenant Alenko rolls his eyes in my general direction and makes the short walk over to the kitchen area, opens the refrigeration chamber, and pulls out a couple of pre-prepared sandwiches. We keep plenty of plain military rations aboard the Normandy, naturally, but the crew can't be blamed for wanting something with flavor every once in a while, and we make sure to restock on groceries every time we pass by someplace with an actual economy.

As Kaidan returns to the table and sits down across from me, I catch movement in the corner of my vision and a door opens off to my left. Garrus Vakarian steps out of the office he has taken to using as his private quarters. He waves a taloned hand in our direction and starts over to the table.

"Everyone's nervous this morning," Kaidan half-whispers, leaning toward me. "I think more than a few of us are wondering what's going to happen to the rest of us when the Council gives you your new mission." He glances over his shoulder at Garrus, favoring the turian with an encouraging smile as he approaches.

When I met Garrus Vakarian, shortly before becoming a Spectre, he was an officer at Citadel Security frustrated by the red tape he had to go through to get the job done. He jumped at the chance to join up with me - so eagerly so that I was hesitant to trust him, but he's proven himself at least a hundred times since then. He helped me take down Saren, and was right there beside me while I was fighting through the small army of the mechanical platforms that the rogue Spectre brought with him when he returned to the Citadel.

In the years since, as we have sought in vain for any information we could find about the Reapers, Garrus has become increasingly focused on learning about not only the Reapers themselves, but anybody else who might be connected to them - by Indoctrination or misguided self-interest. I've caught a glimpse of his office through that door a few times, although he hasn't ever invited me in and, even though it's my ship, I'm not about to intrude on a crew-member's privacy unless necessary. There are always piles of documents strewn on his desk, some of them taped to the wall above the desk. No red string, of course - black string is standard issue.

"Nothing's going to happen," I tell Kaidan, a bit confused by his suggestion. "Unless the crew doesn't want to take the mission, in which case I would understand. My authority as a Spectre covers all of you as well, as long as you're part of this crew. I don't see why any mission the Council gives me would require otherwise."

When I mention the part about my Spectre authority covering the rest of the crew, Garrus's mouth opens in a grin, the mandibles to either side of his triangular lips twitching horizontally. "That's the part I like the most," he says in a raspy voice when he settles down at the table. "We do what we need to do to get the job done. No questions asked." His posture in the chair is relaxed, leaning with his back away from Kaidan and I, and his feet toward the space between us.

"I'd wait till we know what the job is before getting so excited about getting it done," Kaidan says, glancing to Garrus.

Garrus hardly seems fazed by the foreboding in Kaidan's tone. "Do you think we can convince Tali to come back once we get our new mission?" Tali'Zorah left the crew of the Normandy about a year after our defeat of Saren, returning to the Quarian Migrant Fleet to finish her Pilgrimage and officially become an adult within the Quarian society. I've kept in contact with her - she presented the geth data I helped her retrieve to the Captain of the Neema, losing the _nar_ name she had carried and becoming _vas Neema -_ "crew of the Neema," in the Quarian language. Since then she's risen to the rank of chief engineer aboard that ship.

"I don't think Tali's going to come running back to the Normandy just because Shepard has a shiny new mission to fulfill," Kaidan murmurs. "She's a bit busy. And Urdnot Wrex… we could really use someone like him considering the sort of missions we're likely to get. But…"

"He's got a new fight of his own," I say, picking up my sandwich to take a bite. Grilled vegetables and cheese - a mix of disparate flavors, but somehow not confused or clashing. _Wrex would have hated this sandwich._ Urdnot Wrex left a year and a half after Tali did. In our explorations, we encountered many other Krogan, and Wrex decided that it was about time he set out to unite his people. The unity of the Krogan had long been a wish of his, but he had resigned himself to living the life of a wandering mercenary like so many other Krogan, their species drifting toward an inevitable extinction because of the sterility plague, the Genophage, inflicted upon them.

Created by the Salarians, but administered by Garrus's people, the Genophage marked the beginning of the end of an entire race. But in Wrex's mind, there might be a way to stop the Genophage. We saw the attempts on Virmire to reverse the disease, and though they were intended there to create an army of brainwashed Krogan clones, the proof of concept had been created. The Genophage might one day be cured. But it would be hard to cure Wrex's entire people if they were scattered throughout the galaxy, serving nothing but their next paycheck. So he left, went back to Tuchanka. The last I heard from him, Clan Urdnot was gaining in influence.

I hope that Wrex's plans come to fruition. But at the same time, I do wish that he were still here aboard the Normandy. Him and Tali'Zorah both. They were valuable members of the crew - instrumental in stopping Saren from conquering the Citadel and using it to summon the Reapers from the depths of dark space and bring an end to this cycle.

As I set the remaining half of the sandwich down, Garrus sighs loudly and leans forward, his elbows resting on the table's surface and his hands meeting above, fingers steepled. "I'm sure everything will be fine," he grates. "The Council will send us big heroes off to save the galaxy one more time and along the way we'll find out whatever we can about the Reapers. Maybe locate another Sovereign and blow it right to hell."

"If it were that easy, Saren would still be a hero of Council space," Kaidan insists.

"At least, as much as he ever was," Garrus returns, voice dripping with his trademark snark. "You should have met him before he got Indoctrinated. He was always a brutal bastard."

"Look who's talking." Alenko grunts and takes a bite of his sandwich. I see a flicker of anger cross Garrus's face and consider saying something to end the argument before it can truly begin, but before I get the chance to say anything Garrus opens his mouth.

"I may be… rash sometimes, but I don't hurt civilians. Saren once burned down a civilian town to get to his target. Hundreds died. And that was before he became a tool of the Reapers."

"When did that happen?" Kaidan asks, his normally calm voice suddenly quavering.

I take this opportunity to interrupt. "It was Councillor Anderson's evaluation mission, when he almost became a Spectre. He told me about it when he stepped down as Captain of the Normandy. He thinks Saren did it partially just to keep Anderson out of the Spectres."

"Saren always hated humans," Garrus adds. "After he died the council released his personnel files. They mention a brother killed in the Relay 314 Incident." The turian shrugs. "He held a grudge." _The Relay 314 Incident_. It's better known among humans as the _First Contact War_ \- when humanity first made contact with interstellar society. Relay 314 was deactivated and forbidden by the Council, but the human authorities didn't know that. When the turian armada noticed what the rapidly-expanding humans were doing, they attacked without negotiation. The conflict didn't last long, but it left many humans and turians with an instinctive distrust for the other species.

"In any case, I think I'd better try to get some rest. So should you two, if you're tired at all. I imagine we'll be heading off in a hurry after I get out of my meeting with the Council this afternoon." I finish my sandwich and stand up. "Thank you, Kaidan. Garrus."

"Yeah," Kaidan replies. "I'm not exactly tired. Went to sleep early last night." His tone tells me that's the truth.

"Me too," Garrus says. _His_ tone tells me he's lying. "Kaidan, want to hit the range for a little while?"

"Sure, Garrus. I'd like that."

I leave them to their target practice and return to the crew quarters. Before I enter my cabin, Doctor Chakwas, who is predictably waiting out in the corridor, hands me a single small pill. "Wash it down with water," she tells me, and I wave it away.

"I just needed to clear my head, I think. I'll be fine now. But thank you, Doctor."

"Well, you may as well bring it with you into the cabin, Captain," Chakwas replies. "If you change your mind I won't enjoy the elevator ride back up here from med bay."

"All right." I take the pill and wave my hand in front of the door panel to my cabin, then enter after the door slides open. "Good… morning." I almost said 'good night.'

I am asleep again only minutes after climbing back into bed, and this time I do not dream at all.

At 18 standard hours that day, I find myself in the council chambers on the Citadel, standing on the audience platform - alone, as requested. The Citadel Tower is strangely empty - as I cast around looking for onlookers, I can find none. Normally, the Council chambers are full of people during meetings - people of all species, come to look upon the proceedings of the Council and learn of the galaxy's most important happenings firsthand. Today, the only sound from beyond the seat of the four Councillors is the gurgling of the fountain behind me, along the set of stairs leading down and into the main Presidium area.

Being in this room again, for the first time in five years, brings back harsh memories. Memories of Saren, mostly, but also of the twisted mechanical beast he became moments after ending his own life, more like a Geth than a Turian. I remember his body gathering itself up from the ground where he lay after his death, and leaping into the air, clinging to a wall, lunging at me with a strength that was Sovereign's, not Saren's.

The council chamber has changed since that day. There are now four podiums, not three, for the day I defeated Saren and the Alliance fleet rescued the Destiny Ascension (flagship of the Citadel Fleet, aboard which the Council was stationed) from otherwise-certain destruction, was also the day that humanity was invited to add a representative to the council. And as the hero of the day I was asked to choose that representative.

Our ambassador at that time, Udina, was the obvious choice from a practical standpoint - he had political savvy and was eager to stand up for the galactic interests of humanity. But I never trusted him. Something always seemed off about the way he spoke to others, especially non-humans, as though he thought standing up for our interests meant opposing the interests of all other species in the jurisdiction of the citadel council. So instead, I nominated my former Captain, David Anderson, to stand in Udina's place as Councillor. He might not have understood politics, but as Councillor, all he needed to do was make the right decision for everyone, and I trusted Anderson much more than Udina to do that.

My trust hasn't been misplaced, these past five years. Anderson has been a worthy addition to the Council.

"Commander Cian Shepard," he says with a wide grin as I approach my place. "Captain of the Normandy. Spectre. It's good to see you again, my friend." Anderson's face looks more lined with age than it was when he handed the Normandy's command over to me, but not so much as to make him look unhealthy. If anything, the extra wrinkles have only given him more of an aura of authority.

"It's good to see you, too, Councillor Anderson," I call back, settling into my spot. The other three councillors look much the same as I remember them - except for Valern, the Salarian councillor, who stands bent awkwardly and wears the hood of his robe up over his head, as though to deliberately hide his face. Being one of the short-lived Salarians, he may be nearing the end of his life. I don't know how old he is, in truth, and never bothered to check, but it looks like his age is catching up to him. He is, however, the next to speak.

"Greetings, Shepard. Thank you for coming. This is a sensitive matter; it couldn't be trusted to interstellar communication." Valern's clipped sentences and quick speech - typical for Salarians - make it seem like he is hurrying to end this meeting as quickly as possible. In truth, I know that he's making an effort to speak more slowly. Conversation between salarians is often bewilderingly quick and impossible for members of other species to follow - they have extremely fast metabolisms, which is the cause both of their short lifespans and of their quick-moving, quick-thinking tendencies.

Tevos, the Asari councillor, continues. "As you have, most likely, already guessed, we have decided to recall you to fulfill another mission as Council Spectre. For this mission, you are the only qualified Spectre there is - for reasons that will soon become clear."

"And," Sparatus says flatly, "Your search for the other Reapers has thus far turned up nothing. Five years, Commander. It is enough to make one wonder if perhaps Sovereign was the only one of its kind."

"This is unlikely, however," Valern cuts in. Sparatus frowns in response to that, but then shrugs.

"Yes. Unlikely, but nonetheless we feel that it is time for you to take on a new mission as Spectre. Perhaps along the way you will encounter information regarding the other Reapers, if they are still a threat."

"As long as they exist, they're a threat," I return. Sparatus was always the most doubtful of the council, least inclined to trust me. But I can't really blame him, to be truthful. I came into my Spectre status by accusing a renowned turian Spectre of treason, and the turian Councillor still doesn't like thinking that one of his own people, a people proud of their discipline and the achievements that discipline has brought, would turn traitor - Reaper Indoctrination or no. "But I do see your point. Wandering the edges of the galaxy has turned up no more than rumors."

Anderson speaks up next. "Your new assignment can only be completed by you, Shepard, as you are still the only human among the ranks of the Spectres. Are you familiar with an organization calling itself Cerberus?" I can hear the distasteful twist in his voice as he says that name.

 _Cerberus?_ I've met them before, fought them, and they never seemed to be much of a serious threat to galactic peace. They are a human fringe group which wants to elevate humans above all other species in the galaxy. I've actually received direct communication from them before - an anonymous message claiming to represent Cerberus, at least. The message said that I should have used the opportunity provided by Saren's attack on the Citadel to depose the Citadel Council and put an all-human council in its place. Based on what I know about Cerberus, they are crazy, paranoid, obsessed with the supposed superiority of humanity to all others in the galaxy - and so incompetent in their terrorist plans that it is almost comical.

"These terrorists were once beneath our notice," Sparatus clarifies, "But they have become more bold. There are rumblings that they are planning something big. We want you to infiltrate them."

Anderson nods and continues explaining. "Cerberus was found to be interfering in the Ascension project, a biotics research project, at Grissom Academy. One of the students there was a plant, being drugged by agents of Cerberus to create a biotic superweapon of sorts. Gillian Grayson was a proof of concept for Cerberus. They may have lost their 'weapon,' but her exceptional abilities prove that whatever they were doing, it works."

Tevos glances to Anderson and then back toward me. "We fear that Cerberus will attempt to raise an army of biotics like Grayson, and use them in their terrorist actions. That is why we need a Spectre to infiltrate Cerberus - and given their policies, only a human can successfully infiltrate them. Whatever means you consider necessary, take them. We want you to become a spy within Cerberus. Climb their ranks if you can. You have three main objectives in this mission: Find out what Cerberus is planning. Sabotage their plans. And if you can, eliminate their leader.

"Cerberus is held together by a single individual, known to his followers as the Illusive Man. Most of his operatives only know of the existence of a few others, while he pulls all the strings. So, if the Illusive Man is removed from the equation, it is not too much to expect that Cerberus will simply dissolve, lacking orders to carry out."

"You want me to kill this 'Illusive Man'? I ask." _Illusive Man? What a stupid moniker. This clown doesn't sound very smart._

"Yes," Sparatus says flatly.

" _If_ that proves necessary," Valern cuts in. "You could also capture him, which would allow us to learn everything we need to about Cerberus's operations. Assuming that a man like this would cooperate, which is, admittedly, rather unlikely. Assassination would be an effective way to end the threat, but you don't have to go in assuming that is what's necessary. Your methods are, after all, up to you."

"Alright," I reply. "Now, what about my crew? Cerberus won't deal with non-humans, but Garrus Vakarian and Liara T'Soni are valued operatives."

"You should maintain contact with your crew and co-operate with them on missions, while excluding them from any meetings you may have with other Cerberus operatives," Tevos says. "If the question comes up, you can mention them as mercenaries under your command. Cerberus won't bring non-humans into their fold, but they don't have a problem with hiring mercenaries from other species."

"For ideological terrorists," Sparatus says in his dry voice, "They are awfully pragmatic in their approach to solving problems."

I nod. "Any leads as to where I should start?"

Anderson's face twists into a grimace. "There's a procedure for joining Cerberus," he says. "It's been broadcast in Cerberus propaganda. So, they're probably expecting anyone who tries to join might be a mole. You might have to carry out some missions against the interests of citadel space as a whole to gain the trust of Cerberus, but we're hoping that, out in the Terminus Systems, you won't have to do anything of the sort. You need to go to Omega and wait at a reserved table in the Afterlife bar. I'll send a map of the place to the Normandy so you know exactly where to go. There's a guard standing watch over that table at all times - tell them you're there to speak to the Illusive Man and you'll get a meeting via vidscreen, and a mission."

"So," I say doubtfully, "You want me to work for terrorists to stop them? How do I know that the Illusive Man will let me know anything about Cerberus no matter how much work I do for them? If I were him, I'd want to take advantage of any potential spies, especially with a public recruiting announcement like that. I'd give them one mission after another but never offer them any more information than they need to finish the mission, and never give them my trust. I'd use them."

"The Illusive Man is known to meet with his operatives in person on occasion, even the lowest ranking of them," Anderson explains. "Always under heavy guard, of course, but I'm sure you'll figure out something. And any mission he gives you, you are authorized to complete if necessary. We would prefer that you try to sabotage Cerberus activities, but you also need to get close to the Illusive Man if you're going to stop Cerberus. So, keep that in mind."

"Good luck on your mission, Shepard," offers Tevos. "This meeting of the Council is now adjourned."

And with that, I am dismissed. I turn from my place before the Council's platform and begin the long walk down the staircase from the Citadel Tower into the main area of the Presidium.


End file.
